Zinc in PDB 4k3n: Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum

The structure of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum, PDB code: 4k3n was solved by S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.11 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	173.716, 177.079, 229.185, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum (pdb code 4k3n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum, PDB code: 4k3n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:37.6 occ:1.00 OD2 A:ASP399 2.0 9.3 1.0 OE2 A:GLU461 2.1 7.2 1.0 N1 A:1OT1004 2.3 14.3 1.0 NZ A:LYS374 2.3 8.8 1.0 O1 A:1OT1004 2.4 5.1 1.0 OD2 A:ASP379 2.5 8.0 1.0 CG A:ASP399 2.9 8.6 1.0 C1 A:1OT1004 3.1 15.1 1.0 CE A:LYS374 3.1 7.6 1.0 CD A:GLU461 3.1 8.6 1.0 OD1 A:ASP399 3.2 8.7 1.0 ZN A:ZN1003 3.2 46.3 1.0 P A:1OT1004 3.2 13.8 1.0 CG A:ASP379 3.3 5.8 1.0 OE1 A:GLU461 3.4 6.7 1.0 O2 A:CO31002 3.8 7.0 1.0 O2 A:1OT1004 3.8 9.6 1.0 CB A:ASP379 3.9 5.8 1.0 OD1 A:ASP379 4.2 9.2 1.0 CB A:ASP399 4.3 7.4 1.0 O A:THR486 4.4 11.7 1.0 C2 A:1OT1004 4.4 18.4 1.0 CD A:LYS374 4.5 9.9 1.0 CG A:GLU461 4.5 6.0 1.0 CG1 A:ILE376 4.6 9.1 1.0 O3 A:1OT1004 4.7 12.2 1.0 N A:GLY462 4.7 8.6 1.0 CB A:ILE376 4.8 11.3 1.0 CG2 A:ILE376 4.8 9.8 1.0 O A:ASP459 4.9 14.1 1.0 CA A:GLY462 5.0 10.7 1.0

Zinc binding site 2 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:46.3 occ:1.00 OD1 A:ASP459 2.2 10.9 1.0 OD2 A:ASP379 2.2 8.0 1.0 O2 A:1OT1004 2.2 9.6 1.0 O A:ASP459 2.2 14.1 1.0 OE1 A:GLU461 2.3 6.7 1.0 O1 A:1OT1004 2.3 5.1 1.0 P A:1OT1004 2.8 13.8 1.0 CG A:ASP459 3.1 11.8 1.0 CG A:ASP379 3.1 5.8 1.0 C A:ASP459 3.1 5.9 1.0 ZN A:ZN1001 3.2 37.6 1.0 OD1 A:ASP379 3.2 9.2 1.0 CD A:GLU461 3.3 8.6 1.0 OE2 A:GLU461 3.5 7.2 1.0 CA A:ASP459 3.5 11.3 1.0 NZ A:LYS386 3.7 12.4 1.0 CB A:ASP459 3.8 11.2 1.0 OD2 A:ASP459 3.9 17.1 1.0 O3 A:1OT1004 3.9 12.2 1.0 N1 A:1OT1004 4.0 14.3 1.0 CE A:LYS386 4.1 9.1 1.0 C1 A:1OT1004 4.1 15.1 1.0 O2 A:CO31002 4.2 7.0 1.0 N A:ALA460 4.3 8.5 1.0 N A:GLU461 4.4 7.6 1.0 CB A:ASP379 4.5 5.8 1.0 CG A:GLU461 4.7 6.0 1.0 CA A:ALA460 4.7 6.0 1.0 ND2 A:ASN432 4.8 8.0 1.0 OD2 A:ASP399 4.9 9.3 1.0 N A:ASP459 4.9 5.8 1.0 CA A:GLY381 4.9 5.7 1.0

Zinc binding site 3 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:36.5 occ:1.00 OD2 B:ASP399 2.1 12.1 1.0 OE2 B:GLU461 2.2 12.3 1.0 OD2 B:ASP379 2.3 9.0 1.0 O1 B:1OT1004 2.3 9.7 1.0 N1 B:1OT1004 2.3 14.8 1.0 NZ B:LYS374 2.4 6.6 1.0 CG B:ASP399 3.0 11.4 1.0 C1 B:1OT1004 3.1 14.2 1.0 ZN B:ZN1003 3.1 38.3 1.0 P B:1OT1004 3.2 16.0 1.0 CD B:GLU461 3.2 8.6 1.0 CE B:LYS374 3.3 5.4 1.0 OD1 B:ASP399 3.3 10.5 1.0 CG B:ASP379 3.3 10.0 1.0 OE1 B:GLU461 3.5 9.7 1.0 O2 B:CO31002 3.8 7.2 1.0 CB B:ASP379 3.8 7.4 1.0 O2 B:1OT1004 3.9 16.5 1.0 OD1 B:ASP379 4.2 5.2 1.0 CB B:ASP399 4.3 8.6 1.0 O B:THR486 4.4 9.8 1.0 C2 B:1OT1004 4.4 18.1 1.0 CG B:GLU461 4.6 5.4 1.0 O3 B:1OT1004 4.6 18.8 1.0 CD B:LYS374 4.7 5.4 1.0 CG1 B:ILE376 4.7 8.1 1.0 N B:GLY462 4.8 5.4 1.0 O B:ASP459 4.9 7.3 1.0 CB B:ILE376 4.9 9.3 1.0 CG2 B:ILE376 5.0 5.4 1.0

Zinc binding site 4 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:38.3 occ:1.00 OD1 B:ASP459 2.2 7.1 1.0 O B:ASP459 2.2 7.3 1.0 OD2 B:ASP379 2.3 9.0 1.0 OE1 B:GLU461 2.3 9.7 1.0 O1 B:1OT1004 2.3 9.7 1.0 O2 B:1OT1004 2.5 16.5 1.0 P B:1OT1004 2.9 16.0 1.0 CG B:ASP379 3.1 10.0 1.0 CG B:ASP459 3.1 7.6 1.0 C B:ASP459 3.1 9.0 1.0 OD1 B:ASP379 3.1 5.2 1.0 ZN B:ZN1001 3.1 36.5 1.0 CD B:GLU461 3.2 8.6 1.0 OE2 B:GLU461 3.4 12.3 1.0 CA B:ASP459 3.5 7.4 1.0 NZ B:LYS386 3.8 12.2 1.0 CB B:ASP459 3.9 5.5 1.0 OD2 B:ASP459 3.9 13.3 1.0 O3 B:1OT1004 4.0 18.8 1.0 CE B:LYS386 4.1 8.3 1.0 N1 B:1OT1004 4.1 14.8 1.0 O2 B:CO31002 4.2 7.2 1.0 N B:ALA460 4.2 11.2 1.0 N B:GLU461 4.3 7.2 1.0 C1 B:1OT1004 4.3 14.2 1.0 CB B:ASP379 4.5 7.4 1.0 CG B:GLU461 4.5 5.4 1.0 ND2 B:ASN432 4.6 8.1 1.0 CA B:ALA460 4.6 9.8 1.0 OD2 B:ASP399 4.8 12.1 1.0 CA B:GLY381 4.8 9.4 1.0 N B:ASP459 4.9 5.7 1.0 CB B:GLU461 5.0 6.5 1.0

Zinc binding site 5 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:41.8 occ:1.00 OD2 C:ASP399 2.0 14.7 1.0 N1 C:1OT1004 2.3 11.7 1.0 OE2 C:GLU461 2.3 13.8 1.0 O1 C:1OT1004 2.4 17.7 1.0 NZ C:LYS374 2.4 5.5 1.0 OD2 C:ASP379 2.4 6.6 1.0 CG C:ASP399 2.9 12.2 1.0 C1 C:1OT1004 3.1 9.4 1.0 OD1 C:ASP399 3.2 10.1 1.0 P C:1OT1004 3.2 17.3 1.0 ZN C:ZN1003 3.2 41.6 1.0 CD C:GLU461 3.3 10.5 1.0 CE C:LYS374 3.3 3.5 1.0 CG C:ASP379 3.3 8.5 1.0 OE1 C:GLU461 3.5 5.1 1.0 CB C:ASP379 3.8 9.4 1.0 O2 C:1OT1004 3.8 19.0 1.0 O1 C:CO31002 3.8 10.9 1.0 OD1 C:ASP379 4.3 8.6 1.0 CB C:ASP399 4.3 9.4 1.0 O C:THR486 4.4 6.5 1.0 C2 C:1OT1004 4.4 18.1 1.0 O3 C:1OT1004 4.6 18.9 1.0 CG C:GLU461 4.7 4.2 1.0 CD C:LYS374 4.7 4.9 1.0 N C:GLY462 4.8 6.9 1.0 CG1 C:ILE376 4.8 3.6 1.0 O C:ASP459 4.9 4.5 1.0 CB C:ILE376 4.9 3.6 1.0

Zinc binding site 6 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:41.6 occ:1.00 OD2 C:ASP379 2.2 6.6 1.0 OD1 C:ASP459 2.2 8.5 1.0 O C:ASP459 2.2 4.5 1.0 OE1 C:GLU461 2.3 5.1 1.0 O1 C:1OT1004 2.3 17.7 1.0 O2 C:1OT1004 2.5 19.0 1.0 P C:1OT1004 3.0 17.3 1.0 CG C:ASP379 3.0 8.5 1.0 C C:ASP459 3.1 8.3 1.0 CG C:ASP459 3.2 10.9 1.0 ZN C:ZN1001 3.2 41.8 1.0 OD1 C:ASP379 3.2 8.6 1.0 CD C:GLU461 3.2 10.5 1.0 OE2 C:GLU461 3.5 13.8 1.0 CA C:ASP459 3.5 8.8 1.0 NZ C:LYS386 3.7 8.6 1.0 CB C:ASP459 3.9 9.4 1.0 CE C:LYS386 4.0 6.7 1.0 O3 C:1OT1004 4.0 18.9 1.0 OD2 C:ASP459 4.0 12.6 1.0 N C:ALA460 4.2 10.6 1.0 N1 C:1OT1004 4.3 11.7 1.0 O1 C:CO31002 4.3 10.9 1.0 N C:GLU461 4.3 6.1 1.0 C1 C:1OT1004 4.3 9.4 1.0 CB C:ASP379 4.4 9.4 1.0 ND2 C:ASN432 4.6 3.9 1.0 CA C:ALA460 4.6 7.9 1.0 CG C:GLU461 4.6 4.2 1.0 CA C:GLY381 4.8 9.1 1.0 N C:ASP459 4.9 5.8 1.0 OD2 C:ASP399 4.9 14.7 1.0 O C:THR458 5.0 5.5 1.0 C24 C:1PE1008 5.0 43.6 1.0

Zinc binding site 7 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:36.8 occ:1.00 OD2 D:ASP399 2.1 13.1 1.0 OE2 D:GLU461 2.2 4.2 1.0 N1 D:1OT1004 2.3 14.1 1.0 NZ D:LYS374 2.4 5.5 1.0 O3 D:1OT1004 2.4 12.6 1.0 OD2 D:ASP379 2.4 8.3 1.0 CG D:ASP399 2.9 10.8 1.0 ZN D:ZN1003 3.2 45.2 1.0 OD1 D:ASP399 3.2 10.8 1.0 CE D:LYS374 3.2 9.0 1.0 C1 D:1OT1004 3.2 15.4 1.0 CD D:GLU461 3.2 11.2 1.0 P D:1OT1004 3.2 15.3 1.0 CG D:ASP379 3.3 9.5 1.0 OE1 D:GLU461 3.5 5.1 1.0 O1 D:1OT1004 3.7 20.0 1.0 O1 D:CO31002 3.8 10.2 1.0 CB D:ASP379 3.9 11.0 1.0 OD1 D:ASP379 4.2 8.9 1.0 CB D:ASP399 4.3 5.5 1.0 O D:THR486 4.3 9.0 1.0 C2 D:1OT1004 4.5 19.1 1.0 CD D:LYS374 4.6 9.4 1.0 CG D:GLU461 4.6 4.2 1.0 O2 D:1OT1004 4.7 18.2 1.0 CG1 D:ILE376 4.7 8.1 1.0 N D:GLY462 4.8 8.1 1.0 O D:ASP459 4.9 14.0 1.0 CB D:ILE376 4.9 6.5 1.0

Zinc binding site 8 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1003 b:45.2 occ:1.00 OD1 D:ASP459 2.2 10.2 1.0 OD2 D:ASP379 2.2 8.3 1.0 O D:ASP459 2.3 14.0 1.0 OE1 D:GLU461 2.3 5.1 1.0 O3 D:1OT1004 2.3 12.6 1.0 O1 D:1OT1004 2.4 20.0 1.0 P D:1OT1004 2.9 15.3 1.0 CG D:ASP379 3.0 9.5 1.0 C D:ASP459 3.1 6.8 1.0 OD1 D:ASP379 3.1 8.9 1.0 CG D:ASP459 3.1 7.2 1.0 ZN D:ZN1001 3.2 36.8 1.0 CD D:GLU461 3.2 11.2 1.0 OE2 D:GLU461 3.4 4.2 1.0 CA D:ASP459 3.5 6.5 1.0 NZ D:LYS386 3.8 9.8 1.0 CB D:ASP459 3.8 5.8 1.0 OD2 D:ASP459 4.0 6.7 1.0 O2 D:1OT1004 4.0 18.2 1.0 O1 D:CO31002 4.1 10.2 1.0 N1 D:1OT1004 4.1 14.1 1.0 CE D:LYS386 4.2 8.4 1.0 N D:ALA460 4.2 5.6 1.0 C1 D:1OT1004 4.2 15.4 1.0 N D:GLU461 4.4 4.7 1.0 CB D:ASP379 4.4 11.0 1.0 CG D:GLU461 4.6 4.2 1.0 ND2 D:ASN432 4.6 9.1 1.0 CA D:ALA460 4.7 4.7 1.0 CA D:GLY381 4.8 4.1 1.0 OD2 D:ASP399 4.8 13.1 1.0 N D:ASP459 4.9 4.1 1.0

Zinc binding site 9 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:36.8 occ:1.00 OD2 E:ASP399 2.1 13.1 1.0 OE2 E:GLU461 2.2 7.4 1.0 NZ E:LYS374 2.2 5.3 1.0 O1 E:1OT1004 2.3 16.5 1.0 N1 E:1OT1004 2.4 17.1 1.0 OD2 E:ASP379 2.5 5.5 1.0 CG E:ASP399 2.9 13.4 1.0 CE E:LYS374 3.1 6.0 1.0 OD1 E:ASP399 3.1 12.4 1.0 C1 E:1OT1004 3.2 20.3 1.0 CD E:GLU461 3.2 9.7 1.0 P E:1OT1004 3.2 15.3 1.0 ZN E:ZN1003 3.3 49.6 1.0 CG E:ASP379 3.4 6.1 1.0 OE1 E:GLU461 3.5 7.5 1.0 O3 E:CO31002 3.7 11.4 1.0 O2 E:1OT1004 3.9 14.7 1.0 CB E:ASP379 4.0 7.7 1.0 OD1 E:ASP379 4.3 7.8 1.0 O E:THR486 4.3 9.2 1.0 CB E:ASP399 4.3 4.2 1.0 C2 E:1OT1004 4.5 24.5 1.0 CD E:LYS374 4.5 6.8 1.0 CG E:GLU461 4.5 6.9 1.0 O3 E:1OT1004 4.6 20.1 1.0 CG1 E:ILE376 4.7 17.0 1.0 N E:GLY462 4.7 8.3 1.0 O E:ASP459 4.9 4.3 1.0 CB E:ILE376 4.9 12.0 1.0 CA E:GLY462 4.9 6.4 1.0 C E:CO31002 5.0 10.1 1.0

Zinc binding site 10 out of 24 in the Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Phosphonic Arginine Mimetics As Inhibitors of the M17 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1003 b:49.6 occ:1.00 OD1 E:ASP459 2.2 12.8 1.0 OE1 E:GLU461 2.2 7.5 1.0 O E:ASP459 2.2 4.3 1.0 OD2 E:ASP379 2.3 5.5 1.0 O1 E:1OT1004 2.5 16.5 1.0 O2 E:1OT1004 2.6 14.7 1.0 C E:ASP459 3.0 9.9 1.0 CG E:ASP379 3.0 6.1 1.0 CG E:ASP459 3.1 10.6 1.0 P E:1OT1004 3.1 15.3 1.0 OD1 E:ASP379 3.1 7.8 1.0 CD E:GLU461 3.2 9.7 1.0 ZN E:ZN1001 3.3 36.8 1.0 CA E:ASP459 3.4 10.3 1.0 OE2 E:GLU461 3.4 7.4 1.0 NZ E:LYS386 3.7 5.8 1.0 CB E:ASP459 3.8 12.3 1.0 OD2 E:ASP459 3.9 10.4 1.0 CE E:LYS386 4.1 12.0 1.0 O3 E:1OT1004 4.2 20.1 1.0 N E:ALA460 4.2 7.6 1.0 O3 E:CO31002 4.3 11.4 1.0 N E:GLU461 4.3 7.3 1.0 N1 E:1OT1004 4.3 17.1 1.0 C1 E:1OT1004 4.4 20.3 1.0 CB E:ASP379 4.5 7.7 1.0 CG E:GLU461 4.5 6.9 1.0 ND2 E:ASN432 4.5 4.5 1.0 CA E:ALA460 4.6 8.4 1.0 CA E:GLY381 4.7 8.2 1.0 N E:ASP459 4.8 7.3 1.0 OD2 E:ASP399 4.9 13.1 1.0 O E:THR458 4.9 9.8 1.0 CB E:GLU461 5.0 7.7 1.0

K.Kannan Sivaraman, A.Paiardini, M.Sienczyk, C.Ruggeri, C.A.Oellig, J.P.Dalton, P.J.Scammells, M.Drag, S.Mcgowan. Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics As Inhibitors of the M1 and M17 Aminopeptidases From Plasmodium Falciparum. J.Med.Chem. V. 56 5213 2013.
ISSN: ISSN 0022-2623
PubMed: 23713488
DOI: 10.1021/JM4005972